Transition between [R]- and [S]-Stereoisomers without Bond Breaking

We for the first time shown that transition between (R) and (S) stereoisomers via a planar transition state or an intermediate structure without having to break a bond is possible. Rigorous theoretical calculations have been used to study this novel phenomenon and to characterize the energetic, structure, dynamic and kinetic properties

Dispersion Interactions between Urea and Nucleobases Contribute to the Destabilization of RNA by Urea in Aqueous Solution

Urea has long been used to investigate protein folding and, more recently, RNA folding. Studies have proposed that urea denatures RNA by participating in stacking interactions and hydrogen bonds with nucleic acid bases. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated using <i>ab initio</i> calculations (RI-MP2 and CCSD­(T) methods with the aug-cc-pVDZ basis set). A total of 29 stable nucleobase-urea stacked complexes are identified in which the intermolecular interaction energies (up to −14 kcal/mol) are dominated by dispersion effects. Natural bond orbital (NBO) and atoms in molecules (AIM) calculations further confirm strong interactions between urea and nucleobases. Calculations on model systems with multiple urea and water molecules interacting with a guanine base lead to a hypothesis that urea molecules along with water are able to form cage-like structures capable of trapping nucleic acid bases in extrahelical states by forming both hydrogen-bonded and dispersion interactions, thereby contributing to the unfolding of RNA in the presence of urea in aqueous solution